Ribosomal perturbation as a mechanism to prevent misfolding of CFTR

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Abstract Cystic Fibrosis (CF) is a common lethal autosomal recessive disorder, occurring in 1 per 2,500 to 3,500 U.S. births annually. The disease is caused by defects in the CF transmembrane conductance regulator (CFTR). Mutations that change the CFTR coding sequence alter integrity of peptide folding and lead to disease. In this project, we show that CFTR codon alterations—including both non-synonymous and synonymous polymorphisms on background of the common F508del variant—can perturb ribosome dynamics, consequent mRNA utilization, translational rate, and protein biogenesis. The critical relationship between protein folding and translational velocity is a topical area with ramifications ranging from basic CFTR trafficking to disease phenotype and intervention. Mechanistic underpinnings for this application are derived from genome-wide phenomic screening with the Saccharomyces cerevisiae deletion strain library to identify novel modulators of F508del CFTR maturation, leading to discovery of specific ribosomal protein modules that impact F508del CFTR folding. We have established that suppression of Rpl12, along with other 60S proteins comprising the ribosomal stalk, improve F508del CFTR processing and activity at the mammalian cell surface to levels (in primary airway epithelia) predicted to confer clinical benefit among CF patients and comparable in magnitude to lumacaftor, a new agent recently approved for this purpose. Our preliminary data indicate that improved folding and activity of F508del CFTR are attributable to effects on translational kinetics. We propose three Specific Aims to develop an innovative model relevant to CF pathogenesis: 1) Define ribosomal domains and functional pathway interactions that govern ∆F protein biogenesis, and expand the analysis to include other CFTR variants and complex alleles, 2) Ascertain the mechanism by which Rpl12 suppression rescues F508del CFTR function, including relevance of translation rate to disease causing CF mutations and other CFTR polymorphisms, 3) Determine in vivo significance by development of RPL12 conditional knockout or haplosufficient mice. Our team combines multidisciplinary and mutually reinforcing expertise in CFTR biochemistry, transport physiology, ribosome profiling, translational velocity, yeast phenomics, and molecular genetics to mechanistically address a fundamental hypothesis regarding ways the ribosome utilizes mRNA to influence folding and functional quality of resulting gene products. We will establish translation control as a novel and critical mediator of Yor1 and CFTR maturation, identify specific ribosome modules that influence the CFTR biogenesis pathway, and evaluate relevance and safety of repressing this target in a murine disease model. Such results will improve understanding of CF molecular mechanism, suggest novel approaches for personalized treatment of CF patients with the most common forms of the disease, and indicate clinical significance of an important new observation relevant to aberrant protein translation and a fatal genetic illness.